| Added by | celine.gongora |
|---|---|
| Last modified by | standudu |
| Group name | EquipeCG |
| Item Type | Journal Article |
| Title | Analytical Validation of Multiplex Biomarker Assay to Stratify Colorectal Cancer into Molecular Subtypes |
| Creator | Ragulan et al. |
| Author | Chanthirika Ragulan |
| Author | Katherine Eason |
| Author | Elisa Fontana |
| Author | Gift Nyamundanda |
| Author | Noelia Tarazona |
| Author | Yatish Patil |
| Author | Pawan Poudel |
| Author | Rita T. Lawlor |
| Author | Maguy Del Rio |
| Author | Si-Lin Koo |
| Author | Wah-Siew Tan |
| Author | Francesco Sclafani |
| Author | Ruwaida Begum |
| Author | Larissa S. Teixeira Mendes |
| Author | Pierre Martineau |
| Author | Aldo Scarpa |
| Author | Andrés Cervantes |
| Author | Iain Beehuat Tan |
| Author | David Cunningham |
| Author | Anguraj Sadanandam |
| Abstract | Previously, we classified colorectal cancers (CRCs) into five CRCAssigner (CRCA) subtypes with different prognoses and potential treatment responses, later consolidated into four consensus molecular subtypes (CMS). Here we demonstrate the analytical development and validation of a custom NanoString nCounter platform-based biomarker assay (NanoCRCA) to stratify CRCs into subtypes. To reduce costs, we switched from the standard nCounter protocol to a custom modified protocol. The assay included a reduced 38-gene panel that was selected using an in-house machine-learning pipeline. We applied NanoCRCA to 413 samples from 355 CRC patients. From the fresh frozen samples (n?=?237), a subset had matched microarray/RNAseq profiles (n?=?47) or formalin-fixed paraffin-embedded (FFPE) samples (n?=?58). We also analyzed a further 118 FFPE samples. We compared the assay results with the CMS classifier, different platforms (microarrays/RNAseq) and gene-set classifiers (38 and the original 786 genes). The standard and modified protocols showed high correlation (>?0.88) for gene expression. Technical replicates were highly correlated (>?0.96). NanoCRCA classified fresh frozen and FFPE samples into all five CRCA subtypes with consistent classification of selected matched fresh frozen/FFPE samples. We demonstrate high and significant subtype concordance across protocols (100%), gene sets (95%), platforms (87%) and with CMS subtypes (75%) when evaluated across multiple datasets. Overall, our NanoCRCA assay with further validation may facilitate prospective validation of CRC subtypes in clinical trials and beyond. |
| Publication | Scientific Reports |
| Volume | 9 |
| Issue | 1 |
| Pages | 7665 |
| Date | May 21, 2019 |
| Journal Abbr | Sci Rep |
| Language | eng |
| DOI | 10.1038/s41598-019-43492-0 |
| ISSN | 2045-2322 |
| Library Catalog | PubMed |
| Extra | 00000 PMID: 31113981 PMCID: PMC6529539 |
| Tags | original |
| Date Added | 2019/10/10 - 10:40:47 |
| Date Modified | 2019/10/22 - 15:20:42 |
| Notes and Attachments | PubMed entry (Attachment) Texte intégral (Attachment) |
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